X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=dbba0f4cad6b18711cb3824c1022c7d40255a00f;hb=0619c67b9d65ffbe0a7ea5b2c7e12df5d125c535;hp=42e8847fb301940d3c88188fc0c7ec9748b0d38b;hpb=3385d3fe7b3acd45dc5aaa3c7d73f7cce5ea7457;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 42e8847..dbba0f4 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -15,6 +15,7 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ + package jalview.analysis; import java.util.*; @@ -57,11 +58,15 @@ public class StructureFrequency */ public static int findPair(SequenceFeature[] pairs, int indice) { + for (int i = 0; i < pairs.length; i++) { if (pairs[i].getBegin() == indice) + { + return pairs[i].getEnd(); + } } return -1; @@ -82,16 +87,18 @@ public class StructureFrequency int end, Hashtable[] result, boolean profile, AlignmentAnnotation rnaStruc) { + Hashtable residueHash; String maxResidue; - char[] seq, struc = rnaStruc.getRNAStruc().toCharArray(); + char[] struc = rnaStruc.getRNAStruc().toCharArray(); + SequenceFeature[] rna = rnaStruc._rnasecstr; char c, s, cEnd; - int count, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length; + int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length; int[] values; int[][] pairs; float percentage; - + boolean wooble = true; for (i = start; i < end; i++) // foreach column { residueHash = new Hashtable(); @@ -99,9 +106,11 @@ public class StructureFrequency values = new int[255]; pairs = new int[255][255]; bpEnd = -1; + // System.out.println("s="+struc[i]); if (i < struc.length) { s = struc[i]; + } else { @@ -112,7 +121,7 @@ public class StructureFrequency s = '-'; } - if (s != '(') + if (s != '(' && s != '[') { if (s == '-') { @@ -121,19 +130,21 @@ public class StructureFrequency } else { - for (j = 0; j < jSize; j++) // foreach row - { - if (sequences[j] == null) - { - System.err - .println("WARNING: Consensus skipping null sequence - possible race condition."); - continue; - } - seq = sequences[j].getSequence(); - if (seq.length > i) + bpEnd = findPair(rna, i); + + if (bpEnd > -1) + { + for (j = 0; j < jSize; j++) // foreach row { - c = seq[i]; + if (sequences[j] == null) + { + System.err + .println("WARNING: Consensus skipping null sequence - possible race condition."); + continue; + } + c = sequences[j].getCharAt(i); + // System.out.println("c="+c); // standard representation for gaps in sequence and structure if (c == '.' || c == ' ') @@ -146,15 +157,26 @@ public class StructureFrequency values['-']++; continue; } - bpEnd = findPair(rna, i); - cEnd = seq[bpEnd]; - if (checkBpType(c, cEnd)) + cEnd = sequences[j].getCharAt(bpEnd); + + // System.out.println("pairs ="+c+","+cEnd); + if (checkBpType(c, cEnd) == true) { values['(']++; // H means it's a helix (structured) + maxResidue = "("; + wooble = true; + // System.out.println("It's a pair wc"); + + } + if (checkBpType(c, cEnd) == false) + { + wooble = false; + values['[']++; // H means it's a helix (structured) + maxResidue = "["; + } pairs[c][cEnd]++; - maxResidue = "("; } } // nonGap++; @@ -168,13 +190,18 @@ public class StructureFrequency residueHash.put(PAIRPROFILE, pairs); } - - count = values['(']; - + if (wooble == true) + { + count = values['(']; + } + if (wooble == false) + { + count = values['[']; + } residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); - percentage = ((float) count * 100) / (float) jSize; + percentage = ((float) count * 100) / jSize; residueHash.put(PID_GAPS, new Float(percentage)); // percentage = ((float) count * 100) / (float) nongap; @@ -186,11 +213,20 @@ public class StructureFrequency if (bpEnd > 0) { values[')'] = values['(']; + values[']'] = values['[']; values['('] = 0; - + values['['] = 0; residueHash = new Hashtable(); - maxResidue = ")"; - + if (wooble == true) + { + // System.out.println(maxResidue+","+wooble); + maxResidue = ")"; + } + if (wooble == false) + { + // System.out.println(maxResidue+","+wooble); + maxResidue = "]"; + } if (profile) { residueHash.put(PROFILE, new int[][] @@ -203,10 +239,11 @@ public class StructureFrequency residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); - percentage = ((float) count * 100) / (float) jSize; + percentage = ((float) count * 100) / jSize; residueHash.put(PID_GAPS, new Float(percentage)); result[bpEnd] = residueHash; + } } } @@ -309,7 +346,8 @@ public class StructureFrequency } for (int i = iStart; i < width; i++) { - if (i >= hconsensus.length) + Hashtable hci; + if (i >= hconsensus.length || ((hci = hconsensus[i]) == null)) { // happens if sequences calculated over were shorter than alignment // width @@ -317,30 +355,31 @@ public class StructureFrequency continue; } value = 0; + Float fv; if (ignoreGapsInConsensusCalculation) { - value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS)) - .floatValue(); + fv = (Float) hci.get(StructureFrequency.PID_NOGAPS); } else { - value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS)) - .floatValue(); + fv = (Float) hci.get(StructureFrequency.PID_GAPS); } - - String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE) - + " "; + if (fv == null) + { + consensus.annotations[i] = null; + // data has changed below us .. give up and + continue; + } + value = fv.floatValue(); + String maxRes = hci.get(StructureFrequency.MAXRESIDUE).toString(); + String mouseOver = hci.get(StructureFrequency.MAXRESIDUE) + " "; if (maxRes.length() > 1) { mouseOver = "[" + maxRes + "] "; maxRes = "+"; } - int[][] profile = (int[][]) hconsensus[i] - .get(StructureFrequency.PROFILE); - int[][] pairs = (int[][]) hconsensus[i] - .get(StructureFrequency.PAIRPROFILE); + int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE); + int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE); if (pairs != null && includeAllConsSymbols) // Just responsible for the // tooltip @@ -348,7 +387,9 @@ public class StructureFrequency { mouseOver = ""; - /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure? + /* + * TODO It's not sure what is the purpose of the alphabet and wheter it + * is useful for structure? * * if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) { * tval = ((float) profile[0][alphabet[c]]) 100f / (float) @@ -365,7 +406,7 @@ public class StructureFrequency { ca[x] = new int[] { c, d }; - vl[x] = (float) pairs[c][d]; + vl[x] = pairs[c][d]; x++; } } @@ -376,7 +417,7 @@ public class StructureFrequency { if (vl[c] > 0) { - tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0] + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%"; @@ -405,7 +446,7 @@ public class StructureFrequency public static int[] extractProfile(Hashtable hconsensus, boolean ignoreGapsInConsensusCalculation) { - int[] rtnval = new int[51]; // 2*(5*5)+1 + int[] rtnval = new int[74]; // 2*(5*5)+2 int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); int[][] pairs = (int[][]) hconsensus .get(StructureFrequency.PAIRPROFILE); @@ -423,21 +464,23 @@ public class StructureFrequency { ca[x] = new int[] { c, d }; - vl[x] = (float) pairs[c][d]; + vl[x] = pairs[c][d]; x++; } } jalview.util.QuickSort.sort(vl, ca); - rtnval[0] = 1; + rtnval[0] = 2; + rtnval[1] = 0; for (int c = 624; c > 0; c--) { if (vl[c] > 0) { rtnval[rtnval[0]++] = ((int[]) ca[c])[0]; rtnval[rtnval[0]++] = ((int[]) ca[c])[1]; - rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); + rtnval[1] += rtnval[rtnval[0]++]; } }